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I get asked this question all the time and never no how to respond. May one of y'all knows the answer. If a person is preparing DNA, is it necessary to perform RNAse treatment prior to amplifying the 16S gene (say V4 to run on miseq)? Asked another way: will the presence of RNA interfere with or skew the community profile of DNA used for NGS metagenomic community profiling?
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For PCR based amplification of 16S variable regions RNase treatment usually is not necessary. It will impact correct quantification by spectrophotometric methods if it is included in the workflow. If the same extracted DNA will be used for other applications as well it is better to include RNase in one of extraction steps.
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